3QTF

Design and SAR of macrocyclic Hsp90 inhibitors with increased metabolic stability and potent cell-proliferation activity

• PDB DOI: https://doi.org/10.2210/pdb3QTF/pdb

• Classification: CHAPERONE/CHAPERONE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-22 Released: 2011-04-06 
• Deposition Author(s): Zapf, C.W., Bloom, J.D., McBean, J.L., Dushin, R.G., Nittoli, T., Ingalls, C., Sutherland, A.G., Sonye, J.P., Eid, C.N., Golas, J., Liu, H., Boschelli, F., Hu, Y., Vogan, E.M., Levin, J.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.204 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

Design and SAR of macrocyclic Hsp90 inhibitors with increased metabolic stability and potent cell-proliferation activity.

Zapf, C.W., Bloom, J.D., McBean, J.L., Dushin, R.G., Nittoli, T., Ingalls, C., Sutherland, A.G., Sonye, J.P., Eid, C.N., Golas, J., Liu, H., Boschelli, F., Hu, Y., Vogan, E., Levin, J.I.

(2011) Bioorg Med Chem Lett 21: 2278-2282

• PubMed: 21420297 
• DOI: https://doi.org/10.1016/j.bmcl.2011.02.101
• Primary Citation of Related Structures:  
  3QTF


• PubMed Abstract: 
  

  A novel series of macrocyclic ortho-aminobenzamide Hsp90 inhibitors is reported. A basic nitrogen within the tether linking the aniline nitrogen atom to a tetrahydroindolone moiety allowed access to compounds with good physical properties. Important structure-activity relationship information was obtained from this series which led to the discovery of a soluble and stable compound which is potent in an Hsp90 binding and cell-proliferation assay.

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Organizational Affiliation: 

Medicinal Chemistry, Pfizer, 401 N. Middletown Road, Pearl River, NY 10965, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.9 kDa 
• Atom Count: 1,985 
• Modelled Residue Count: 207 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	226	Homo sapiens	Mutation(s): 0  Gene Names: HSP90A, HSP90AA1, HSPC1, HSPCA EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens) Explore P07900  Go to UniProtKB:  P07900
PHAROS:  P07900 GTEx:  ENSG00000080824

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
05S	B [auth A]	(6S)-6,15,15,18-tetramethyl-17-oxo-2,3,4,5,6,7,14,15,16,17-decahydro-1H-8,12-(metheno)[1,4,9]triazacyclotetradecino[9,8-a]indole-9-carboxamide C24 H32 N4 O2 DGOVAFNEOBXFEF-AWEZNQCLSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
05S	BindingDB:  3QTF	IC50: 110 (nM) from 1 assay(s)
	PDBBind:  3QTF	IC50: 110 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.204 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.264	α = 90
b = 90.718	β = 90
c = 98.379	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Zapf, C.W., Bloom, J.D., McBean, J.L., Dushin, R.G., Nittoli, T., Ingalls, C., Sutherland, A.G., Sonye, J.P., Eid, C.N., Golas, J., Liu, H., Boschelli, F., Hu, Y., Vogan, E.M., Levin, J.I.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations